Template directed split and mix synthesis of small molecule libraries

1. A method for synthesizing an encoded molecule comprising the steps of:

a) Adding a linker molecule L to one or more reaction wells;

b) Adding a molecule fragment to each of said reaction wells;

c) Adding an oligonucleotide identifier to each of said reaction wells;

d) Subjecting said wells to:

conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or

conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers;

e) Combining the contents of said one or more reaction wells;

wherein at least one reactive group of the linker molecule L reacts with a reactive group in the molecule fragment, or with a reactive group in the oligonucleotide;

wherein at least one reactive group of the molecule fragments reacts with a reactive group in the linker molecule L, or with a reactive group in another molecule fragment,

wherein at least one reactive group of the oligonucleotide identifiers reacts with a reactive group in the linker L, or with a reactive group in another oligonucleotide identifier; and

wherein the region of the oligonucleotide identifier added to each well in step c), which hybridizes to said template identifies the molecule fragment added to the same well in step b).